Inputs and parameters
Parameters
- Run functional and taxonomic annotations Yes
- Run MEGAN Yes
- Run annotations with COGs Yes
- Build submission files Yes
- Run blast against your own fasta file No
Annotation
Result table
| Prokka Fasta files | Prokka annotation | Diamond fosmid against NR | Diamond fosmid against Uniprot | Diamond ORFs against NR | Diamond ORFs against Uniprot | COGs annotation |
|---|---|---|---|---|---|---|
| DNA - PROT | GFF | TSV | TSV | TSV | TSV | RPSBLAST |
Result table by fosmid
| Sample | Length | GC% | A | T | G | C | Others | Prokka | GenBank | Annotated ORFs against Uniprot |
Annotated ORFs against NR |
MEGAN | COGs | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| bioindent1.C1a | 38297 | 44.24 | 8711 | 12643 | 7822 | 9121 | 0 | Fasta | GBK | 5 / 41 | 17 / 41 | Function unknown | ||||
| bioindent2.C1 | 37094 | 37.26 | 11696 | 11578 | 7119 | 6701 | 0 | Fasta | GBK | 15 / 44 | 36 / 44 | Amino acid transport and metabolism | ||||
Produced by MEGAN5
bioindent1.C1a
Based on Diamond results of each ORF against NR, details for each annotated ORFs (17/41)
| ORF | HSP | Max coverage | Best HSP (max. of %iden * coverage) | ||
|---|---|---|---|---|---|
| %iden. | Coverage | Species | |||
| ORF2 | 7 |
98.5%
|
35.1 |
93.5%
|
Treponema azotonutricium |
| ORF4 | 211 |
98.0%
|
28.5 |
92.2%
|
Thermodesulfitimonas autotrophica |
| ORF8 | 1000 |
99.6%
|
45.3 |
99.2%
|
Spirochaeta lutea |
| ORF14 | 1000 |
71.2%
|
47.7 |
60.5%
|
Treponema maltophilum |
| ORF18 | 1000 |
99.2%
|
49.2 |
96.1%
|
Bacteroidales bacterium Barb7 |
| ORF21 | 122 |
99.1%
|
65.7 |
99.1%
|
Candidatus Termititenax aidoneus |
| ORF24 | 17 |
98.1%
|
39.9 |
98.1%
|
Treponema azotonutricium |
| ORF26 | 1 |
51.6%
|
36.0 |
51.6%
|
Proteobacteria bacterium CAG:495 |
| ORF28 | 193 |
77.5%
|
45.8 |
77.2%
|
Treponema primitia |
| ORF29 | 816 |
99.6%
|
58.5 |
99.6%
|
Treponema primitia |
| ORF30 | 437 |
99.8%
|
62.1 |
99.8%
|
Treponema primitia |
| ORF32 | 44 |
97.5%
|
54.9 |
97.5%
|
Treponema primitia |
| ORF35 | 1000 |
99.3%
|
42.1 |
98.2%
|
Clostridium sp. AF18-27 |
| ORF36 | 3 |
76.7%
|
25.6 |
76.7%
|
Ruminococcaceae bacterium YRB3002 |
| ORF37 | 1 |
89.5%
|
37.4 |
89.5%
|
Gottschalkiaceae bacterium |
| ORF39 | 1000 |
98.0%
|
31.8 |
98.0%
|
uncultured bacterium |
| ORF40 | 3 |
88.4%
|
37.6 |
88.4%
|
Treponema primitia |
bioindent2.C1
Based on Diamond results of each ORF against NR, details for each annotated ORFs (36/44)
| ORF | HSP | Max coverage | Best HSP (max. of %iden * coverage) | ||
|---|---|---|---|---|---|
| %iden. | Coverage | Species | |||
| ORF1 | 1000 |
99.3%
|
78.1 |
82.8%
|
uncultured bacterium |
| ORF2 | 1000 |
99.5%
|
54.7 |
98.1%
|
Bifidobacterium stellenboschense |
| ORF3 | 1000 |
99.5%
|
63.6 |
95.8%
|
Kineothrix alysoides |
| ORF4 | 1000 |
99.6%
|
66.3 |
97.8%
|
Kineothrix alysoides |
| ORF5 | 988 |
99.8%
|
34.2 |
99.0%
|
Clostridiales bacterium Marseille-P2846 |
| ORF6 | 916 |
99.4%
|
73.9 |
97.0%
|
Treponema primitia |
| ORF7 | 1000 |
99.6%
|
49.4 |
96.3%
|
Treponema caldarium |
| ORF8 | 3 |
96.6%
|
27.0 |
96.6%
|
Treponema azotonutricium |
| ORF9 | 1000 |
99.6%
|
71.9 |
96.1%
|
Deltaproteobacteria bacterium |
| ORF10 | 1000 |
99.1%
|
66.1 |
99.1%
|
Treponema primitia |
| ORF11 | 79 |
95.8%
|
63.4 |
86.3%
|
Treponema primitia |
| ORF12 | 1000 |
94.9%
|
54.9 |
78.8%
|
Methanobrevibacter gottschalkii |
| ORF14 | 108 |
95.2%
|
46.7 |
91.7%
|
Methyloversatilis discipulorum |
| ORF15 | 9 |
59.4%
|
36.4 |
53.8%
|
Geobacillus sp. 12AMOR1 |
| ORF17 | 8 |
96.2%
|
33.8 |
93.9%
|
Candidatus Micrarchaeota archaeon |
| ORF18 | 1 |
51.0%
|
34.2 |
51.0%
|
Flavobacteriales bacterium CG_4_10_14_0_8_um_filter_32_5 |
| ORF19 | 96 |
99.4%
|
50.5 |
98.7%
|
Riemerella anatipestifer |
| ORF20 | 13 |
99.5%
|
46.6 |
99.5%
|
Treponema primitia |
| ORF22 | 4 |
99.4%
|
36.2 |
99.4%
|
Treponema putidum |
| ORF24 | 1000 |
87.7%
|
52.4 |
76.1%
|
Algoriphagus yeomjeoni |
| ORF26 | 5 |
79.5%
|
40.6 |
79.5%
|
Flavobacterium aciduliphilum |
| ORF28 | 22 |
94.6%
|
66.3 |
93.5%
|
Treponema pedis |
| ORF30 | 10 |
66.7%
|
71.7 |
66.7%
|
Treponema pedis |
| ORF31 | 1000 |
99.6%
|
83.0 |
99.3%
|
Treponema primitia |
| ORF32 | 1000 |
95.4%
|
73.4 |
94.4%
|
Treponema primitia |
| ORF33 | 1000 |
99.5%
|
75.8 |
98.1%
|
Treponema primitia |
| ORF34 | 1000 |
99.6%
|
82.0 |
99.6%
|
Treponema primitia |
| ORF36 | 197 |
97.9%
|
52.9 |
96.5%
|
Desulfosporosinus sp. BG |
| ORF37 | 1000 |
99.9%
|
54.1 |
99.8%
|
Desulfosporosinus sp. BG |
| ORF38 | 52 |
99.5%
|
67.8 |
94.5%
|
Paenibacillus pasadenensis |
| ORF39 | 147 |
99.8%
|
57.6 |
99.8%
|
Desulfosporosinus sp. BG |
| ORF40 | 1000 |
99.6%
|
70.2 |
99.2%
|
uncultured Flavonifractor sp. |
| ORF41 | 1000 |
99.5%
|
73.8 |
99.1%
|
Ruminococcus sp. CAG:724 |
| ORF42 | 1000 |
99.3%
|
54.6 |
96.6%
|
Ruminococcus sp. CAG:724 |
| ORF43 | 1000 |
98.9%
|
60.2 |
98.4%
|
Treponema primitia |
bioindent1.C1a
Based on Diamond results of each ORF against NR, details for each annotated ORFs (5/41)
| ORF | HSP | Max coverage | Best HSP (max. of %iden * coverage) | ||
|---|---|---|---|---|---|
| %iden. | Coverage | Species | |||
| ORF4 | 2 |
62.7%
|
27.5 |
62.7%
|
Escherichia coli |
| ORF8 | 3 |
99.2%
|
42.0 |
99.2%
|
Treponema pallidum |
| ORF14 | 528 |
67.5%
|
39.2 |
59.8%
|
Rhodopseudomonas palustris |
| ORF35 | 1 |
81.1%
|
27.1 |
81.1%
|
Staphylococcus xylosus |
| ORF39 | 6 |
61.8%
|
37.8 |
57.9%
|
Clostridium cellulovorans |
bioindent2.C1
Based on Diamond results of each ORF against NR, details for each annotated ORFs (15/44)
| ORF | HSP | Max coverage | Best HSP (max. of %iden * coverage) | ||
|---|---|---|---|---|---|
| %iden. | Coverage | Species | |||
| ORF1 | 12 |
99.3%
|
40.1 |
99.3%
|
Clostridium thermocellum |
| ORF2 | 1 |
84.7%
|
27.2 |
84.7%
|
Escherichia coli |
| ORF3 | 184 |
99.5%
|
62.6 |
94.4%
|
Clostridium botulinum |
| ORF4 | 228 |
99.6%
|
60.2 |
96.7%
|
Clostridium cellulolyticum |
| ORF7 | 65 |
99.6%
|
36.4 |
98.8%
|
Bradyrhizobium sp |
| ORF9 | 1 |
96.9%
|
38.2 |
96.9%
|
Escherichia coli |
| ORF10 | 3 |
96.6%
|
32.1 |
96.6%
|
Mycobacterium bovis |
| ORF12 | 19 |
81.2%
|
39.9 |
81.2%
|
Bacillus subtilis |
| ORF31 | 31 |
98.6%
|
37.2 |
98.2%
|
Thermodesulfovibrio yellowstonii |
| ORF32 | 360 |
94.4%
|
52.0 |
92.6%
|
Lactobacillus casei |
| ORF33 | 217 |
99.5%
|
44.7 |
98.6%
|
Moorella thermoacetica |
| ORF34 | 683 |
99.6%
|
56.3 |
98.5%
|
Marinobacter hydrocarbonoclasticus |
| ORF40 | 1000 |
99.6%
|
51.8 |
98.1%
|
Bacillus subtilis |
| ORF41 | 9 |
95.4%
|
38.1 |
95.4%
|
Bacillus subtilis |
| ORF42 | 2 |
94.4%
|
31.4 |
94.4%
|
Bacillus subtilis |
bioindent1.C1a
Based on Rps-Blast results against COGs database, details for each COGs categories found.
| COGs category | ORFs | COGs (Best hit) |
|---|---|---|
| Function unknown | ORF6 | COG4642, Uncharacterized protein conserved in bacteria | ORF7 | COG4642, Uncharacterized protein conserved in bacteria | ORF9 | COG4642, Uncharacterized protein conserved in bacteria | ORF10 | COG4642, Uncharacterized protein conserved in bacteria | ORF12 | COG4642, Uncharacterized protein conserved in bacteria | ORF22 | COG4642, Uncharacterized protein conserved in bacteria | ORF27 | COG4642, Uncharacterized protein conserved in bacteria |
| General function prediction only | ORF13 | COG0457, NrfG, FOG: TPR repeat | ORF26 | COG0790, FOG: TPR repeat, SEL1 subfamily | ORF29 | COG4245, TerY, Uncharacterized protein encoded in toxicity protection region of plasmid R478, contains von Willebrand factor (vWF) domain | ORF30 | COG0515, SPS1, Serine/threonine protein kinase [General function prediction only / Signal transduction mechanisms / Transcription / DNA replication, recombination, and repair] | ORF31 | COG0790, FOG: TPR repeat, SEL1 subfamily |
| Carbohydrate transport and metabolism | ORF14 | COG3839, MalK, ABC-type sugar transport systems, ATPase components | ORF39 | COG2730, BglC, Endoglucanase |
| Cell motility and secretion | ORF4 | COG1536, FliG, Flagellar motor switch protein | ORF8 | COG1868, FliM, Flagellar motor switch protein |
| Signal transduction mechanisms | ORF18 | COG3744, PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) | ORF21 | COG2337, MazF, Growth inhibitor |
| Cell envelope biogenesis, outer membrane | ORF28 | COG3064, TolA, Membrane protein involved in colicin uptake |
| Posttranslational modification, protein turnover, chaperones | ORF23 | COG0484, DnaJ, DnaJ-class molecular chaperone with C-terminal Zn finger domain |
| Transcription | ORF35 | COG2207, AraC, AraC-type DNA-binding domain-containing proteins |
bioindent2.C1
Based on Rps-Blast results against COGs database, details for each COGs categories found.
| COGs category | ORFs | COGs (Best hit) |
|---|---|---|
| Amino acid transport and metabolism | ORF31 | COG0040, HisG, ATP phosphoribosyltransferase | ORF32 | COG0131, HisB, Imidazoleglycerol-phosphate dehydratase | ORF33 | COG0118, HisH, Glutamine amidotransferase | ORF34 | COG0107, HisF, Imidazoleglycerol-phosphate synthase | ORF40 | COG1126, GlnQ, ABC-type polar amino acid transport system, ATPase component | ORF41 | COG0765, HisM, ABC-type amino acid transport system, permease component | ORF42 | COG0834, HisJ, ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms] |
| General function prediction only | ORF2 | COG0637, Predicted phosphatase/phosphohexomutase | ORF5 | COG4552, Eis, Predicted acetyltransferase involved in intracellular survival and related acetyltransferases | ORF9 | COG4804, Predicted nuclease of restriction endonuclease-like fold | ORF24 | COG4551, Predicted protein tyrosine phosphatase | ORF27 | COG0666, Arp, FOG: Ankyrin repeat |
| Function unknown | ORF15 | COG3680, Uncharacterized protein conserved in bacteria | ORF28 | COG3514, Uncharacterized protein conserved in bacteria |
| Transcription | ORF6 | COG1329, Transcriptional regulators, similar to M. xanthus CarD | ORF43 | COG1595, RpoE, DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog |
| Coenzyme metabolism | ORF3 | COG0352, ThiE, Thiamine monophosphate synthase | ORF4 | COG2145, ThiM, Hydroxyethylthiazole kinase, sugar kinase family |
| Posttranslational modification, protein turnover, chaperones | ORF12 | COG0464, SpoVK, ATPases of the AAA+ class |
| Cell division and chromosome partitioning | ORF37 | COG1196, Smc, Chromosome segregation ATPases |
| Lipid metabolism | ORF7 | COG1211, IspD, 4-diphosphocytidyl-2-methyl-D-erithritol synthase |
| Carbohydrate transport and metabolism | ORF1 | COG2730, BglC, Endoglucanase |
| Signal transduction mechanisms | ORF10 | COG2337, MazF, Growth inhibitor |